Research workbench
Structure of a seleno-methionyl derivative of wild type arabinofuranosidase from thermobacillus xylanilyticus
Analyse Structure of a seleno-methionyl derivative of wild type arabinofuranosidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VRK
- Type
- protein
- Length
- 1,479 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-arabinofuranosidase
- EC
- 3.2.1.55
- UniProt
- O69262
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 493 | 30% helix, 30% strand | O69262 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.83 | 0.84 | 87 | empty |
| 2 | 484 | 0.74 | 0.83 | 42 | empty |
| 3 | 676 | 0.74 | 0.80 | 59 | empty |
| 4 | 199 | 0.51 | 0.77 | 24 | empty |
| 5 | 70 | 0.40 | 0.79 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 937 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 918 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 916 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 modified, 3 disulfide (engineered, disulfide).
Compared structures
- 2VRK · Structure of a seleno-methionyl derivative of wild type arabinofuranosidase from… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O69262
- Elsewhere: RCSB PDB 2VRK · PDBe 2VRK · UniProt O69262
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